Hello again
and update in the topic.
I just performed a clean install without the option
"-DMINICONDA_USE_PY3=TRUE" which according to the manual should not
change anything
But now, make install has finished without the error.
However now, amber.pip does not even exists.
And the make tests.serial still finishes with the same error:
==============================================================
Testing the Python LES API
/sharelab/labapps/AMBER/CentOS-8-NOPY3/Amber20//miniconda/bin/python test.py
Could not import sanderles. Skipping test
Could not import the compiled Python-sander interface. Make sure you
have the Python development libraries installed and that you have
sourced amber.sh or amber.cshmake[2]: Leaving directory
'/sharelab/labapps/AMBER/CentOS-8-NOPY3/Amber20/test/sanderlesapi'
make[1]: Leaving directory
'/sharelab/labapps/AMBER/CentOS-8-NOPY3/Amber20/test/sanderlesapi'
thank you very much for your help
OCS
Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
mail: ocs.bioinf.uab.es
telf:0034 93586 8939; 0034 93581 4431
On 13/9/21 12:51, Oscar Conchillo-Solé wrote:
> Hello everybody
>
> I just found the same problem presented in this thread and here I
> cannot see it solved:
> http://archive.ambermd.org/202106/0165.html
>
> answering your questions:
>
> 1 (ls -l of amber.pip)
> lrwxrwxrwx 1 ocs users 58 Sep 10 14:37
> /sharelab/labapps/AMBER/CentOS-8/Amber20/bin/amber.pip ->
> /sharelab/labapps/AMBER/CentOS-8/Amber20/miniconda/bin/pip
> (empty link,
> /sharelab/labapps/AMBER/CentOS-8/Amber20/miniconda/bin/pip des not
> exists)
>
>
> 2 (ls -l of miniconda dir) (long list here)
> [ocs.mrb-39-118 Amber20]$ ls -l
> /sharelab/labapps/AMBER/CentOS-8/Amber20/miniconda/bin/
> total 73028
> lrwxrwxrwx 1 ocs users 8 Sep 10 14:35 2to3 -> 2to3-3.9
> -rwxrwxr-x 1 ocs users 170 Sep 10 14:12 2to3-3.9
> -rwxrwxr-x 1 ocs users 253 Sep 10 14:13 activate
> -rwxrwxr-x 1 ocs users 1136480 Dec 12 2018 assistant
> -rwxrwxr-x 1 ocs users 38176 Oct 12 2020 brotli
> -rwxrwxr-x 1 ocs users 97680 Apr 18 2020 bsdcat
> -rwxrwxr-x 1 ocs users 809448 Apr 18 2020 bsdcpio
> -rwxrwxr-x 1 ocs users 868464 Apr 18 2020 bsdtar
> -rwxrwxr-x 1 ocs users 110256 Jul 15 2019 bunzip2
> -rwxrwxr-x 1 ocs users 110256 Jul 15 2019 bzcat
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 bzcmp -> bzdiff
> -rwxrwxr-x 1 ocs users 2140 Jul 15 2019 bzdiff
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 bzegrep -> bzgrep
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 bzfgrep -> bzgrep
> -rwxrwxr-x 1 ocs users 2054 Jul 15 2019 bzgrep
> -rwxrwxr-x 1 ocs users 110256 Jul 15 2019 bzip2
> -rwxrwxr-x 1 ocs users 21064 Jul 15 2019 bzip2recover
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 bzless -> bzmore
> -rwxrwxr-x 1 ocs users 1259 Jul 15 2019 bzmore
> -rwxrwxr-x 1 ocs users 6326 Sep 10 14:12 c_rehash
> -rwxrwxr-x 1 ocs users 35768 Dec 12 2018 canbusutil
> lrwxrwxrwx 1 ocs users 3 Sep 10 14:36 captoinfo -> tic
> -rwxrwxr-x 1 ocs users 299 Sep 10 14:13 chardetect
> -rwxrwxr-x 1 ocs users 39552 Nov 9 2017 cjpeg
> -rwxrwxr-x 1 ocs users 14288 Apr 29 2020 clear
> -rwxrwxr-x 1 ocs users 580 Sep 10 14:13 conda
> -rwxrwxr-x 1 ocs users 303 Sep 10 14:14 conda-build
> -rwxrwxr-x 1 ocs users 305 Sep 10 14:14 conda-convert
> -rwxrwxr-x 1 ocs users 303 Sep 10 14:14 conda-debug
> -rwxrwxr-x 1 ocs users 305 Sep 10 14:14 conda-develop
> -rwxrwxr-x 1 ocs users 217 Sep 10 14:13 conda-env
> -rwxrwxr-x 1 ocs users 303 Sep 10 14:14 conda-index
> -rwxrwxr-x 1 ocs users 305 Sep 10 14:14 conda-inspect
> -rwxrwxr-x 1 ocs users 309 Sep 10 14:14 conda-metapackage
> -rwxrwxr-x 1 ocs users 304 Sep 10 14:14 conda-render
> -rwxrwxr-x 1 ocs users 306 Sep 10 14:14 conda-skeleton
> -rwxrwxr-x 1 ocs users 303 Sep 10 14:12 cph
> -rwxrwxr-x 1 ocs users 19800 Mar 18 09:19 curve_keygen
> -rwxrwxr-x 1 ocs users 298 Sep 10 14:13 cygdb
> -rwxrwxr-x 1 ocs users 319 Sep 10 14:13 cython
> -rwxrwxr-x 1 ocs users 299 Sep 10 14:13 cythonize
> -rwxrwxr-x 1 ocs users 20920 Oct 14 2020 dbus-cleanup-sockets
> -rwxrwxr-x 1 ocs users 280640 Sep 10 14:14 dbus-daemon
> -rwxrwxr-x 1 ocs users 34528 Sep 10 14:14 dbus-launch
> -rwxrwxr-x 1 ocs users 35936 Oct 14 2020 dbus-monitor
> -rwxrwxr-x 1 ocs users 20784 Oct 14 2020 dbus-run-session
> -rwxrwxr-x 1 ocs users 40168 Oct 14 2020 dbus-send
> -rwxrwxr-x 1 ocs users 35336 Oct 14 2020 dbus-test-tool
> -rwxrwxr-x 1 ocs users 21232 Oct 14 2020
> dbus-update-activation-environment
> -rwxrwxr-x 1 ocs users 20400 Oct 14 2020 dbus-uuidgen
> -rwxrwxr-x 1 ocs users 341 Sep 10 14:13 deactivate
> -rwxrwxr-x 1 ocs users 38528 Apr 28 2020 derb
> -rwxrwxr-x 1 ocs users 409320 Dec 12 2018 designer
> -rwxrwxr-x 1 ocs users 34936 Nov 9 2017 djpeg
> -rwxrwxr-x 1 ocs users 323 Sep 10 14:13 f2py
> -rwxrwxr-x 1 ocs users 323 Sep 10 14:13 f2py3
> -rwxrwxr-x 1 ocs users 323 Sep 10 14:13 f2py3.9
> -rwxrwxr-x 1 ocs users 130 Sep 10 14:13 f90nml
> -rwxrwxr-x 1 ocs users 34384 Mar 23 10:39 fax2ps
> -rwxrwxr-x 1 ocs users 30072 Mar 23 10:39 fax2tiff
> -rwxrwxr-x 1 ocs users 26000 Feb 4 2021 fc-cache
> -rwxrwxr-x 1 ocs users 25624 Feb 4 2021 fc-cat
> -rwxrwxr-x 1 ocs users 20520 Feb 4 2021 fc-conflist
> -rwxrwxr-x 1 ocs users 20888 Feb 4 2021 fc-list
> -rwxrwxr-x 1 ocs users 25320 Feb 4 2021 fc-match
> -rwxrwxr-x 1 ocs users 20864 Feb 4 2021 fc-pattern
> -rwxrwxr-x 1 ocs users 20696 Feb 4 2021 fc-query
> -rwxrwxr-x 1 ocs users 20912 Feb 4 2021 fc-scan
> -rwxrwxr-x 1 ocs users 25048 Feb 4 2021 fc-validate
> -rwxrwxr-x 1 ocs users 6344 Oct 16 2018 fixqt4headers.pl
> -rwxr-xr-x 1 ocs users 297 Sep 10 14:14 fonttools
> -rwxrwxr-x 1 ocs users 5374 Sep 10 14:14 freetype-config
> -rwxrwxr-x 1 ocs users 23160 Sep 10 14:14 gapplication
> -rwxrwxr-x 1 ocs users 60944 Sep 10 14:14 gdbus
> -rwxrwxr-x 1 ocs users 2117 Sep 10 14:14 gdbus-codegen
> -rwxrwxr-x 1 ocs users 25936 Apr 28 2020 genbrk
> -rwxrwxr-x 1 ocs users 21248 Apr 28 2020 gencfu
> -rwxrwxr-x 1 ocs users 38936 Apr 28 2020 gencnval
> -rwxrwxr-x 1 ocs users 41008 Apr 28 2020 gendict
> -rwxrwxr-x 1 ocs users 148072 Apr 28 2020 genrb
> -rwxrwxr-x 1 ocs users 115512 Sep 10 14:14 gio
> -rwxrwxr-x 1 ocs users 22152 Aug 19 15:59 gio-querymodules
> -rwxrwxr-x 1 ocs users 55768 Sep 10 14:14 glib-compile-resources
> -rwxrwxr-x 1 ocs users 60944 Sep 10 14:14 glib-compile-schemas
> -rwxrwxr-x 1 ocs users 41109 Aug 19 15:58 glib-genmarshal
> -rwxrwxr-x 1 ocs users 5612 Sep 10 14:14 glib-gettextize
> -rwxrwxr-x 1 ocs users 30801 Aug 19 15:58 glib-mkenums
> -rwxrwxr-x 1 ocs users 17288 Aug 19 15:59 gobject-query
> -rwxrwxr-x 1 ocs users 22320 Sep 10 14:14 gresource
> -rwxrwxr-x 1 ocs users 33168 Sep 10 14:14 gsettings
> -rwxrwxr-x 1 ocs users 58544 Jan 5 2021 gst-device-monitor-1.0
> -rwxrwxr-x 1 ocs users 80240 Jan 5 2021 gst-discoverer-1.0
> -rwxrwxr-x 1 ocs users 165120 Jan 5 2021 gst-inspect-1.0
> -rwxrwxr-x 1 ocs users 105680 Jan 5 2021 gst-launch-1.0
> -rwxrwxr-x 1 ocs users 151856 Jan 5 2021 gst-play-1.0
> -rwxrwxr-x 1 ocs users 87672 Jan 5 2021 gst-stats-1.0
> -rwxrwxr-x 1 ocs users 48712 Jan 5 2021 gst-typefind-1.0
> -rwxrwxr-x 1 ocs users 32976 Aug 19 15:59 gtester
> -rwxrwxr-x 1 ocs users 19095 Aug 19 15:58 gtester-report
> -rwxrwxr-x 1 ocs users 22545 Sep 10 14:13 icu-config
> -rwxrwxr-x 1 ocs users 20872 Apr 28 2020 icuinfo
> lrwxrwxrwx 1 ocs users 7 Sep 10 14:35 idle3 -> idle3.9
> -rwxrwxr-x 1 ocs users 168 Sep 10 14:12 idle3.9
> -rwxrwxr-x 1 ocs users 63512 Apr 29 2020 infocmp
> lrwxrwxrwx 1 ocs users 3 Sep 10 14:36 infotocap -> tic
> -rwxrwxr-x 1 ocs users 309 Sep 10 14:14 iptest
> -rwxrwxr-x 1 ocs users 309 Sep 10 14:14 iptest3
> -rwxrwxr-x 1 ocs users 302 Sep 10 14:14 ipython
> -rwxrwxr-x 1 ocs users 302 Sep 10 14:14 ipython3
> -rwxrwxr-x 1 ocs users 43120 Nov 9 2017 jpegtran
> -rwxrwxr-x 1 ocs users 46224 Apr 5 20:51 jpgicc
> -rwxr-xr-x 1 ocs users 293 Sep 10 14:14 jsonschema
> -rwxrwxr-x 1 ocs users 297 Sep 10 14:13 jupyter
> -rwxrwxr-x 1 ocs users 311 Sep 10 14:14 jupyter-bundlerextension
> -rwxr-xr-x 1 ocs users 303 Sep 10 14:14 jupyter-kernel
> -rwxr-xr-x 1 ocs users 341 Sep 10 14:14 jupyter-kernelspec
> -rwxrwxr-x 1 ocs users 297 Sep 10 14:13 jupyter-migrate
> -rwxrwxr-x 1 ocs users 299 Sep 10 14:14 jupyter-nbconvert
> -rwxrwxr-x 1 ocs users 298 Sep 10 14:14 jupyter-nbextension
> -rwxrwxr-x 1 ocs users 297 Sep 10 14:14 jupyter-notebook
> -rwxr-xr-x 1 ocs users 300 Sep 10 14:14 jupyter-run
> -rwxrwxr-x 1 ocs users 302 Sep 10 14:14 jupyter-serverextension
> -rwxrwxr-x 1 ocs users 302 Sep 10 14:13 jupyter-troubleshoot
> -rwxr-xr-x 1 ocs users 332 Sep 10 14:14 jupyter-trust
> -rwxrwxr-x 1 ocs users 184496 Dec 12 2018 lconvert
> lrwxrwxrwx 1 ocs users 15 Sep 10 14:35 libpng-config ->
> libpng16-config
> -rwxrwxr-x 1 ocs users 2396 Sep 10 14:14 libpng16-config
> -rwxrwxr-x 1 ocs users 1080616 Dec 12 2018 linguist
> -rwxrwxr-x 1 ocs users 35424 Apr 5 20:51 linkicc
> -rwxrwxr-x 1 ocs users 336968 Dec 12 2018 lrelease
> -rwxrwxr-x 1 ocs users 632368 Dec 12 2018 lupdate
> -rwxrwxr-x 1 ocs users 345400 Jul 30 16:57 lz4
> lrwxrwxrwx 1 ocs users 3 Sep 10 14:36 lz4c -> lz4
> lrwxrwxrwx 1 ocs users 3 Sep 10 14:35 lz4cat -> lz4
> lrwxrwxrwx 1 ocs users 2 Sep 10 14:35 lzcat -> xz
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 lzcmp -> xzdiff
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 lzdiff -> xzdiff
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 lzegrep -> xzgrep
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 lzfgrep -> xzgrep
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 lzgrep -> xzgrep
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 lzless -> xzless
> lrwxrwxrwx 1 ocs users 2 Sep 10 14:35 lzma -> xz
> -rwxrwxr-x 1 ocs users 21216 Apr 16 2020 lzmadec
> -rwxrwxr-x 1 ocs users 21128 Sep 10 14:12 lzmainfo
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 lzmore -> xzmore
> -rwxrwxr-x 1 ocs users 75464 Apr 28 2020 makeconv
> -rwxrwxr-x 1 ocs users 303 Sep 10 14:13 matplotlib
> -rwxrwxr-x 1 ocs users 924832 Dec 12 2018 moc
> -rwxrwxr-x 1 ocs users 8300 Sep 10 14:12 ncursesw6-config
> -rwxr-xr-x 1 ocs users 324 Sep 10 14:12 normalizer
> -rwxrwxr-x 1 ocs users 833296 Sep 2 16:12 openssl
> -rwxrwxr-x 1 ocs users 144720 Aug 27 19:20 opj_compress
> -rwxrwxr-x 1 ocs users 136472 Aug 27 19:20 opj_decompress
> -rwxrwxr-x 1 ocs users 127488 Aug 27 19:20 opj_dump
> -rwxrwxr-x 1 ocs users 25552 Mar 23 10:39 pal2rgb
> -rwxrwxr-x 1 ocs users 187208 Sep 10 14:13 patchelf
> -rwxrwxr-x 1 ocs users 2432 Sep 10 14:14 pcre-config
> -rwxrwxr-x 1 ocs users 57056 Jun 23 21:50 pcregrep
> -rwxrwxr-x 1 ocs users 83136 Jun 23 21:50 pcretest
> -rwxrwxr-x 1 ocs users 52968 Dec 12 2018 pixeltool
> -rwxrwxr-x 1 ocs users 58304 Apr 28 2020 pkgdata
> -rwxrwxr-x 1 ocs users 296 Sep 10 14:13 pkginfo
> -rwxrwxr-x 1 ocs users 19800 Apr 23 2019 png-fix-itxt
> -rwxrwxr-x 1 ocs users 60440 Apr 23 2019 pngfix
> -rwxrwxr-x 1 ocs users 25592 Mar 23 10:39 ppm2tiff
> -rwxrwxr-x 1 ocs users 25984 Apr 5 20:51 psicc
> -rwxrwxr-x 1 ocs users 300 Sep 10 14:13 py.test
> lrwxrwxrwx 1 ocs users 8 Sep 10 14:35 pydoc -> pydoc3.9
> lrwxrwxrwx 1 ocs users 8 Sep 10 14:36 pydoc3 -> pydoc3.9
> -rwxrwxr-x 1 ocs users 153 Sep 10 14:12 pydoc3.9
> -rwxr-xr-x 1 ocs users 294 Sep 10 14:14 pyftmerge
> -rwxr-xr-x 1 ocs users 295 Sep 10 14:14 pyftsubset
> -rwxr-xr-x 1 ocs users 295 Sep 10 14:14 pygmentize
> -rwxrwxr-x 1 ocs users 140 Sep 10 14:14 pylupdate5
> -rwxrwxr-x 1 ocs users 136 Sep 10 14:14 pyrcc5
> -rwxrwxr-x 1 ocs users 300 Sep 10 14:13 pytest
> lrwxrwxrwx 1 ocs users 9 Sep 10 14:36 python -> python3.9
> lrwxrwxrwx 1 ocs users 9 Sep 10 14:35 python3 -> python3.9
> lrwxrwxrwx 1 ocs users 16 Sep 10 14:36 python3-config ->
> python3.9-config
> -rwxrwxr-x 1 ocs users 15687904 Sep 10 14:12 python3.9
> -rwxrwxr-x 1 ocs users 3669 Sep 10 14:12 python3.9-config
> -rwxrwxr-x 1 ocs users 135 Sep 10 14:14 pyuic5
> -rwxrwxr-x 1 ocs users 56736 Dec 12 2018 qcollectiongenerator
> -rwxrwxr-x 1 ocs users 48504 Dec 12 2018 qdbus
> -rwxrwxr-x 1 ocs users 192104 Dec 12 2018 qdbuscpp2xml
> -rwxrwxr-x 1 ocs users 110968 Dec 12 2018 qdbusviewer
> -rwxrwxr-x 1 ocs users 60512 Dec 12 2018 qdbusxml2cpp
> -rwxrwxr-x 1 ocs users 1052208 Dec 12 2018 qdoc
> -rwxrwxr-x 1 ocs users 5494856 Dec 12 2018 qgltf
> -rwxrwxr-x 1 ocs users 151760 Dec 12 2018 qhelpconverter
> -rwxrwxr-x 1 ocs users 23216 Dec 12 2018 qhelpgenerator
> -rwxrwxr-x 1 ocs users 88880 Dec 12 2018 qlalr
> -rwxrwxr-x 1 ocs users 23349704 Sep 10 14:14 qmake
> -rwxrwxr-x 1 ocs users 56688 Dec 12 2018 qml
> -rwxrwxr-x 1 ocs users 745440 Dec 12 2018 qmlcachegen
> -rwxrwxr-x 1 ocs users 89968 Dec 12 2018 qmleasing
> -rwxrwxr-x 1 ocs users 208592 Dec 12 2018 qmlimportscanner
> -rwxrwxr-x 1 ocs users 170976 Dec 12 2018 qmllint
> -rwxrwxr-x 1 ocs users 72608 Dec 12 2018 qmlmin
> -rwxrwxr-x 1 ocs users 102640 Dec 12 2018 qmlplugindump
> -rwxrwxr-x 1 ocs users 127000 Dec 12 2018 qmlprofiler
> -rwxrwxr-x 1 ocs users 48656 Dec 12 2018 qmlscene
> -rwxrwxr-x 1 ocs users 6312 Dec 12 2018 qmltestrunner
> -rwxrwxr-x 1 ocs users 245648 Dec 12 2018 qscxmlc
> -rwxrwxr-x 1 ocs users 389 Sep 10 14:14 qt.conf
> -rwxrwxr-x 1 ocs users 44152 Dec 12 2018 qtattributionsscanner
> -rwxrwxr-x 1 ocs users 57120 Dec 12 2018 qtdiag
> -rwxrwxr-x 1 ocs users 23112 Dec 12 2018 qtpaths
> -rwxrwxr-x 1 ocs users 23216 Dec 12 2018 qtplugininfo
> -rwxrwxr-x 1 ocs users 1698424 Dec 12 2018 qwebengine_convert_dict
> -rwxrwxr-x 1 ocs users 33632 Mar 23 10:39 raw2tiff
> -rwxrwxr-x 1 ocs users 851024 Dec 12 2018 rcc
> -rwxrwxr-x 1 ocs users 16264 Nov 9 2017 rdjpgcom
> -rwxrwxr-x 1 ocs users 332168 Sep 10 14:14 repc
> lrwxrwxrwx 1 ocs users 4 Sep 10 14:36 reset -> tset
> -rwxrwxr-x 1 ocs users 3882464 Sep 28 2020 rg
> -rwxrwxr-x 1 ocs users 435672 Dec 9 2020 sip
> -rwxrwxr-x 1 ocs users 1588448 Jun 23 19:49 sqlite3
> -rwxrwxr-x 1 ocs users 30301 Jun 18 2020 sqlite3_analyzer
> -rwxrwxr-x 1 ocs users 49240 Oct 16 2018 syncqt.pl
> -rwxrwxr-x 1 ocs users 14280 Apr 29 2020 tabs
> lrwxrwxrwx 1 ocs users 8 Sep 10 14:35 tclsh -> tclsh8.6
> -rwxrwxr-x 1 ocs users 19960 Jun 18 2020 tclsh8.6
> -rwxrwxr-x 1 ocs users 88128 Apr 29 2020 tic
> -rwxrwxr-x 1 ocs users 29776 Mar 23 10:39 tiff2bw
> -rwxrwxr-x 1 ocs users 92168 Mar 23 10:39 tiff2pdf
> -rwxrwxr-x 1 ocs users 66800 Mar 23 10:39 tiff2ps
> -rwxrwxr-x 1 ocs users 29584 Mar 23 10:39 tiff2rgba
> -rwxrwxr-x 1 ocs users 25544 Mar 23 10:39 tiffcmp
> -rwxrwxr-x 1 ocs users 57360 Mar 23 10:39 tiffcp
> -rwxrwxr-x 1 ocs users 123840 Mar 23 10:39 tiffcrop
> -rwxrwxr-x 1 ocs users 25152 Mar 23 10:39 tiffdither
> -rwxrwxr-x 1 ocs users 34352 Mar 23 10:39 tiffdump
> -rwxrwxr-x 1 ocs users 30464 Mar 23 10:39 tiffinfo
> -rwxrwxr-x 1 ocs users 29600 Mar 23 10:39 tiffmedian
> -rwxrwxr-x 1 ocs users 25216 Mar 23 10:39 tiffset
> -rwxrwxr-x 1 ocs users 25072 Mar 23 10:39 tiffsplit
> -rwxrwxr-x 1 ocs users 49600 Apr 5 20:51 tificc
> -rwxrwxr-x 1 ocs users 22472 Apr 29 2020 toe
> -rwxrwxr-x 1 ocs users 22504 Apr 29 2020 tput
> -rwxr-xr-x 1 ocs users 287 Sep 10 14:12 tqdm
> -rwxrwxr-x 1 ocs users 45632 Apr 5 20:51 transicc
> -rwxrwxr-x 1 ocs users 30672 Apr 29 2020 tset
> -rwxr-xr-x 1 ocs users 292 Sep 10 14:14 ttx
> -rwxrwxr-x 1 ocs users 487240 Dec 12 2018 uic
> lrwxrwxrwx 1 ocs users 3 Sep 10 14:36 unlz4 -> lz4
> lrwxrwxrwx 1 ocs users 2 Sep 10 14:36 unlzma -> xz
> lrwxrwxrwx 1 ocs users 2 Sep 10 14:36 unxz -> xz
> lrwxrwxrwx 1 ocs users 4 Sep 10 14:35 unzstd -> zstd
> -rwxrwxr-x 1 ocs users 37520 Feb 1 2021 webpinfo
> -rwxrwxr-x 1 ocs users 43000 Feb 1 2021 webpmux
> lrwxrwxrwx 1 ocs users 7 Sep 10 14:35 wish -> wish8.6
> -rwxrwxr-x 1 ocs users 20112 Jun 18 2020 wish8.6
> -rwxrwxr-x 1 ocs users 16368 Nov 9 2017 wrjpgcom
> -rwxrwxr-x 1 ocs users 2568888 Jun 3 07:35 x86_64-conda-linux-gnu-ld
> lrwxrwxrwx 1 ocs users 25 Sep 10 14:36
> x86_64-conda_cos6-linux-gnu-ld -> x86_64-conda-linux-gnu-ld
> -rwxrwxr-x 1 ocs users 2340 Sep 10 14:13 xml2-config
> -rwxrwxr-x 1 ocs users 27120 Jun 23 21:52 xmlcatalog
> -rwxrwxr-x 1 ocs users 90048 Jun 23 21:52 xmllint
> -rwxrwxr-x 1 ocs users 52392 Dec 12 2018 xmlpatterns
> -rwxrwxr-x 1 ocs users 10608 Dec 12 2018 xmlpatternsvalidator
> -rwxrwxr-x 1 ocs users 45720 May 24 11:44 xmlwf
> -rwxrwxr-x 1 ocs users 99688 Sep 10 14:12 xz
> lrwxrwxrwx 1 ocs users 2 Sep 10 14:35 xzcat -> xz
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 xzcmp -> xzdiff
> -rwxrwxr-x 1 ocs users 21216 Apr 16 2020 xzdec
> -rwxrwxr-x 1 ocs users 6633 Apr 16 2020 xzdiff
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:36 xzegrep -> xzgrep
> lrwxrwxrwx 1 ocs users 6 Sep 10 14:35 xzfgrep -> xzgrep
> -rwxrwxr-x 1 ocs users 5630 Apr 16 2020 xzgrep
> -rwxrwxr-x 1 ocs users 1799 Apr 16 2020 xzless
> -rwxrwxr-x 1 ocs users 2162 Apr 16 2020 xzmore
> -rwxrwxr-x 1 ocs users 182640 Apr 1 00:09 zstd
> lrwxrwxrwx 1 ocs users 4 Sep 10 14:35 zstdcat -> zstd
> -rwxrwxr-x 1 ocs users 3869 Mar 2 2021 zstdgrep
> -rwxrwxr-x 1 ocs users 30 Mar 2 2021 zstdless
> lrwxrwxrwx 1 ocs users 4 Sep 10 14:35 zstdmt -> zstd
>
> here you can find all the output from the cmake; make; make install:
>
> http://bioinf.uab.es/ocs/MISC/amber_install_out.txt
>
>
> If you look at line 346 you will see that the installation of
> charset-normalizer-2.0.4 uninstalled pip-21.1.3-py39h06a4308_0
>
> maybe this is it
>
> on the other hand when I run make test.serial it ends like this:
>
> ==============================================================
> Testing GB sander interface (samecoords w/out RDT)
> PASSED
> ==============================================================
> Testing PME sander interface
> PASSED
> ==============================================================
> Testing the Python LES API
> /sharelab/labapps/AMBER/CentOS-8/Amber20//miniconda/bin/python test.py
> Could not import sanderles. Skipping test
> Could not import the compiled Python-sander interface. Make sure you
> have the Python development libraries installed and that you have
> sourced amber.sh or amber.cshmake[2]: Leaving directory
> '/sharelab/labapps/AMBER/CentOS-8/Amber20/test/sanderlesapi'
> make[1]: Leaving directory
> '/sharelab/labapps/AMBER/CentOS-8/Amber20/test/sanderlesapi'
>
> here the ouptut for make test.serial
> http://bioinf.uab.es/ocs/MISC/tests_out.txt
>
> my commands:
> cmake ../amber20_src
> -DCMAKE_INSTALL_PREFIX=/sharelab/labapps/AMBER/CentOS-8/Amber20
> -DCOMPILER=GNU -DOPENMP=TRUE -DDOWNLOAD_MINICONDA=TRUE
> -DMINICONDA_USE_PY3=TRUE -DINSTALL_TESTS=TRUE
> make
> make install
>
> I'm in a CentOS 8 fully updated machine
>
> thank you very much
>
> OCS
>
>
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Received on Mon Sep 13 2021 - 05:00:02 PDT
